def test_phos_enz2(): a = Agent('MAP2K1') b = Agent('PP2A') st = Dephosphorylation(b, a, 'serine', '222') s = ea._assemble_modification(st) print(s) assert s == 'PP2A dephosphorylates MAP2K1 on S222.'
def test_phos_enz(): a = Agent('MAP2K1') b = Agent('BRAF') st = Phosphorylation(b, a, 'serine', '222') s = ea._assemble_modification(st) print(s) assert s == 'BRAF phosphorylates MAP2K1 on S222.'
def test_deubiq_stmt(): st = Deubiquitination(Agent('X'), Agent('Y')) sb = ea._assemble_modification(st) print(sb.sentence) assert sb.sentence == 'X deubiquitinates Y.' assert _substring_by_coords(sb.sentence, sb.agents[0].coords) == 'X' assert _substring_by_coords(sb.sentence, sb.agents[1].coords) == 'Y'
def test_dephos_no_residue(): a = Agent('MAP2K1') b = Agent('PP2A') st = Dephosphorylation(b, a, None, '222') s = ea._assemble_modification(st) print(s) assert s == 'PP2A dephosphorylates MAP2K1 at position 222.'
def test_phos_noenz3(): a = Agent('MAP2K1') st = Phosphorylation(None, a, 'serine', '222') sb = ea._assemble_modification(st) print(sb.sentence) assert sb.sentence == 'MAP2K1 is phosphorylated on S222.' assert _substring_by_coords(sb.sentence, sb.agents[0].coords) == 'MAP2K1'
def test_phos_indirect(): a = Agent('MAP2K1') b = Agent('BRAF') ev = Evidence(epistemics={'direct': False}) st = Phosphorylation(b, a, 'serine', '222', evidence=[ev]) s = ea._assemble_modification(st) print(s) assert s == 'BRAF leads to the phosphorylation of MAP2K1 on S222.'
def test_dephos_no_residue(): a = Agent('MAP2K1') b = Agent('PP2A') st = Dephosphorylation(b, a, None, '222') sb = ea._assemble_modification(st) print(sb.sentence) assert sb.sentence == 'PP2A dephosphorylates MAP2K1 at position 222.' assert _substring_by_coords(sb.sentence, sb.agents[0].coords) == 'PP2A' assert _substring_by_coords(sb.sentence, sb.agents[1].coords) == 'MAP2K1'
def test_phos_enz2(): a = Agent('MAP2K1') b = Agent('PP2A') st = Dephosphorylation(b, a, 'serine', '222') sb = ea._assemble_modification(st) print(sb.sentence) assert sb.sentence == 'PP2A dephosphorylates MAP2K1 on S222.' assert _substring_by_coords(sb.sentence, sb.agents[0].coords) == 'PP2A' assert _substring_by_coords(sb.sentence, sb.agents[1].coords) == 'MAP2K1'
def test_phos_indirect(): a = Agent('MAP2K1') b = Agent('BRAF') ev = Evidence(epistemics={'direct': False}) st = Phosphorylation(b, a, 'serine', '222', evidence=[ev]) sb = ea._assemble_modification(st) print(sb.sentence) assert sb.sentence == 'BRAF leads to the phosphorylation of MAP2K1 on S222.' assert _substring_by_coords(sb.sentence, sb.agents[0].coords) == 'BRAF' assert _substring_by_coords(sb.sentence, sb.agents[1].coords) == 'MAP2K1'
def test_phos_noenz3(): a = Agent('MAP2K1') st = Phosphorylation(None, a, 'serine', '222') s = ea._assemble_modification(st) print(s) assert s == 'MAP2K1 is phosphorylated on S222.'
def test_phos_noenz(): a = Agent('MAP2K1') st = Phosphorylation(None, a) s = ea._assemble_modification(st) print(s) assert s == 'MAP2K1 is phosphorylated.'
def test_deubiq_noenz(): st = Deubiquitination(None, Agent('Y')) sb = ea._assemble_modification(st) print(sb.sentence) assert sb.sentence == 'Y is deubiquitinated.' assert _substring_by_coords(sb.sentence, sb.agents[0].coords) == 'Y'
def test_deubiq_stmt(): st = Deubiquitination(Agent('X'), Agent('Y')) s = ea._assemble_modification(st) print(s) assert s == 'X deubiquitinates Y.'
def test_deubiq_noenz(): st = Deubiquitination(None, Agent('Y')) s = ea._assemble_modification(st) print(s) assert s == 'Y is deubiquitinated.'